Name: SIGSEGV
No: 11
Description: It is sent from within the the program when it tried to access a memory that is not in it allocated range. The memory management hardwre notice the attempt and inform the kernel which send a SIGSEGV to terminate the program

Thursday, May 27, 2010

Lm-sensors is the low level driver and service that connects to the motherboard components capable of monitoring temperatures and voltages. Lm-sensors collects the data over the reevant subsystem, an I2C interface.

Hardware Prerequisites.
For more information on hardware support by lm_sensors, please visit the Device lm-sensors wiki

Install Prerequisites and XSensors
Step 1: Install lm_sensors package

yum install lm_sensors lm_sensors-devel

Step 2: Install gtk2

yum install gtk+

Step 3:Download the xsensors from the http//linuxhardware.org). The current version at this point in writing is xsensors-0.70.
*Ensure you have GNU compilers installed so that you can compile the program

Thursday, May 13, 2010

BOINC is a program that lets you donate your idle computer time to science projects like SETI@home, Climateprediction.net, Rosetta@home, World Community Grid, and many others. Currently more than 500,000 computers are linked and BIONIC is delivering 5 PetaFlops of Computin Hours! Amazing.

Gentoo, Fedora, Ubuntu and Debian are supported. For more information on installation on Linux, you can read the BIONIC wiki. Installing BOINC
For Fedora, do the following
Install the package using yum

Press the Esc key twice to get to "System Configuration and Boot Management" and then select "Save Settings" and "Exit Setup".

Follow the instructions on the next screen to exit the "Setup Utility".

Power the blade off for the changes to take effect and restart.

Changing "Normal" mode to "Performance" mode affects the way that the Dual In-Line Memory Modules (DIMMs) are refreshed. This results in a DIMM temperature warning message occurring at a 10 degree lower temperature. This causes no impact in most industry standard data centers.

Friday, May 7, 2010

NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently and in its usage of available parallel computing resources. NWChem has been developed by the Molecular Sciences Software group at the Department of Energy's EMSL. Most of the implementation has been funded by the EMSL Construction Project.

Thursday, May 6, 2010

GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation.

Wednesday, May 5, 2010

I was compiling CPMD with OpenMPI, Intel Compilers and MKL on CentOS 5.4. It was tough until I stumble onto this blog Install CPMD by craigb (http://cheminsilico.blogspot.com/). I used the recommendation with minor tweak and it works right out of the box!

The University of Sydney Silica Cluster has also written some information on how to compile CMPD in their environment. For more information take a look at How to compile cpmd (No Gromos QMMM)

Monday, May 3, 2010

It seems that calling Intel MKL routines that are threaded from multiple application threads can lead to conflict (including incorrect answers or program failures) or at best longer unexpected CPU times.

Intel MKL can be aware that it is in a parallel region only if the threaded program and Intel MKL are using the same threading library. If the user program is threaded by some other means, Intel MKL may operate in multithreaded mode and the computations may be corrupted. Here is Intel recommendation
Here are several cases and our recommendations:

User threads the program using OS threads (pthreads on Linux*, Win32* threads on Windows*). If more than one thread calls Intel MKL and the function being called is threaded, it is important that threading in Intel MKL be turned off. Set OMP_NUM_THREADS=1 in the environment.

User threads the program using OpenMP directives and/or pragmas and compiles the program using a compiler other than a compiler from Intel. This is more problematic because setting OMP_NUM_THREADS in the environment affects both the compiler's threading library and the threading library with Intel MKL. In this case, the safe approach is to set OMP_NUM_THREADS=1.

Multiple programs are running on a multiple-CPU system. In cluster applications, the parallel program can run separate instances of the program on each processor. However, the threading software will see multiple processors on the system even though each processor has a separate process running on it. In this case OMP_NUM_THREADS should be set to 1.

If the variable OMP_NUM_THREADS environment variable is not set, then the default number of threads will be assumed 1.

Setting the Number of Threads for OpenMP* (OMP)

The OpenMP* software responds to the environment variable OMP_NUM_THREADS:

Windows*: Open the Environment panel of the System Properties box of the Control Panel on Microsoft* Windows NT*, or it can be set in the shell the program is running in with the command: set OMP_NUM_THREADS=.

Sunday, May 2, 2010

Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft)